Demultiplex Element Biosciences bases files
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
run_manifest:file
RunManifest file
*.{csv}
run_dir:directory
Input run directory containing optionally containing a RunManifest.json if run_manifest is not supplied
sample_fastq
output/Samples/**/*_R*.fastq.gz:file
Demultiplexed sample FASTQ files
output/Samples/*/*_R*.fastq.gz
sample_json
output/Samples/**/*_stats.json:file
Demultiplexed sample stats
output/Samples/*/*.json
qc_report
output/*.html:file
QC HTML report
output/*.html
run_stats
output/RunStats.json:file
generated_run_manifest
output/RunManifest.json:file
Updated Run Manifest JSON from the run_manifest csv
output/RunManifest.json
metrics
output/Metrics.csv:file
Sample metrics
output/Metrics.csv
unassigned
output/UnassignedSequences.csv:file
Unassigned Sequences
output/UnassignedSequences.csv
versions
versions.yml:file
File containing software versions
versions.yml
Demultiplexes sequencing data and converts base calls into FASTQ files for secondary analysis
